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- PDB-9ey6: Crystal structure of human tyrosinase-related protein 1 (TYRP1) -

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Basic information

Entry
Database: PDB / ID: 9ey6
TitleCrystal structure of human tyrosinase-related protein 1 (TYRP1)
Components5,6-dihydroxyindole-2-carboxylic acid oxidase
KeywordsMETAL BINDING PROTEIN / melanogenesis / human tyrosinase / tyrosinase inhibitor
Function / homology
Function and homology information


acetoacetic acid metabolic process / Melanin biosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanocyte differentiation / melanosome membrane / melanosome organization / intracellular vesicle ...acetoacetic acid metabolic process / Melanin biosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanocyte differentiation / melanosome membrane / melanosome organization / intracellular vesicle / Regulation of MITF-M-dependent genes involved in pigmentation / clathrin-coated endocytic vesicle membrane / melanosome / oxidoreductase activity / endosome membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
5,6-dihydroxyindole-2-carboxylic acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.228 Å
AuthorsNg, Y.M. / Soler-Lopez, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847439European Union
CitationJournal: Chembiochem / Year: 2024
Title: Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical tudies.
Authors: Faure, C. / Min Ng, Y. / Belle, C. / Soler-Lopez, M. / Khettabi, L. / Saidi, M. / Berthet, N. / Maresca, M. / Philouze, C. / Rachidi, W. / Reglier, M. / du Moulinet d'Hardemare, A. / Jamet, H.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,22616
Polymers50,7761
Non-polymers4,45015
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-94 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.754, 103.754, 140.988
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5,6-dihydroxyindole-2-carboxylic acid oxidase / DHICA oxidase / Catalase B / Glycoprotein 75 / Melanoma antigen gp75 / Tyrosinase-related protein 1 ...DHICA oxidase / Catalase B / Glycoprotein 75 / Melanoma antigen gp75 / Tyrosinase-related protein 1 / TRP / TRP-1 / TRP1


Mass: 50776.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYRP1, CAS2, TYRP, TYRRP / Plasmid: pACEBac1 / Cell (production host): Insect Cell / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P17643, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor

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Sugars , 5 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 191 molecules

#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, zinc chloride, Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.227→50 Å / Num. obs: 81266 / % possible obs: 99.06 % / Redundancy: 4.4 % / Biso Wilson estimate: 44.72 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1136 / Rpim(I) all: 0.06149 / Rrim(I) all: 0.1295 / Net I/σ(I): 6.55
Reflection shellResolution: 2.24→2.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.158 / Num. unique obs: 3810 / CC1/2: 0.46 / CC star: 0.794 / Rpim(I) all: 0.6229 / % possible all: 86.53

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.228→44.967 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.166 / SU B: 5.179 / SU ML: 0.122 / Average fsc free: 0.9633 / Average fsc work: 0.9743 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 2108 4.939 %RANDOM
Rwork0.1698 40574 --
all0.172 ---
obs-42682 98.043 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.698 Å20.349 Å2-0 Å2
2--0.698 Å20 Å2
3----2.265 Å2
Refinement stepCycle: LAST / Resolution: 2.228→44.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 279 182 4032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124017
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163507
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.8415504
X-RAY DIFFRACTIONr_angle_other_deg0.6621.7548125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.925535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56910561
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19810196
X-RAY DIFFRACTIONr_chiral_restr0.1860.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02974
X-RAY DIFFRACTIONr_nbd_refined0.2180.2774
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.23214
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21984
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1150.21971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3440.24
X-RAY DIFFRACTIONr_metal_ion_refined0.2870.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3750.220
X-RAY DIFFRACTIONr_nbd_other0.2190.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.080.28
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1180.21
X-RAY DIFFRACTIONr_mcbond_it4.7915.0241796
X-RAY DIFFRACTIONr_mcbond_other4.7895.0241796
X-RAY DIFFRACTIONr_mcangle_it6.8999.0342246
X-RAY DIFFRACTIONr_mcangle_other6.8989.0392247
X-RAY DIFFRACTIONr_scbond_it6.7836.0282221
X-RAY DIFFRACTIONr_scbond_other6.7836.0292222
X-RAY DIFFRACTIONr_scangle_it9.83710.8423256
X-RAY DIFFRACTIONr_scangle_other9.83510.8423257
X-RAY DIFFRACTIONr_lrange_it11.17754.4854363
X-RAY DIFFRACTIONr_lrange_other11.19954.0874329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.228-2.2850.348990.29422870.29632050.9190.93974.44620.28
2.285-2.3480.291320.26129340.26230660.9360.9521000.242
2.348-2.4160.2691740.2428340.24130090.9550.96199.96680.218
2.416-2.490.3111350.2327910.23429280.9440.96699.93170.208
2.49-2.5710.2421480.21227050.21428530.9640.9711000.19
2.571-2.6610.2781310.20926180.21227490.9550.9721000.188
2.661-2.7610.2511210.19424940.19726160.9570.97799.96180.174
2.761-2.8730.2321360.17924430.18225790.9640.981000.16
2.873-3.0010.2091500.18423090.18624600.9680.9899.95940.169
3.001-3.1460.2171050.16922450.17123500.9660.9831000.158
3.146-3.3160.1991260.17821150.1822420.9740.98199.95540.17
3.316-3.5160.1921040.17220170.17321220.9780.98499.95290.167
3.516-3.7570.2021160.16618920.16820090.980.98699.95020.163
3.757-4.0550.2081070.14317530.14718600.9780.9871000.146
4.055-4.4390.168780.12516460.12717240.9850.991000.132
4.439-4.9570.177660.12215240.12415920.9830.99199.87440.13
4.957-5.7120.187710.13113370.13414100.9820.9999.85820.139
5.712-6.9680.215510.15211580.15412100.9770.98899.91740.159
6.968-9.7380.168320.1469170.1469500.9830.98699.89470.161
9.738-44.9670.202260.2325550.2315920.9780.95198.14190.305

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